There were a lot of tears in Libreville on Sunday. There were the tears of Pierre-Emerick Aubameyang, overwhelmed by having missed the decisive penalty in Gabon's shootout defeat to Mali and there were the tears of Seydou Keita as he used his side's progress to the semi-final for the first time in 10 years to highlight the crisis overwhelming his country.

Keita began the tournament fronting an Oxfam campaign to raise awareness of the food crisis sweeping the Sahel after a year of poor rains. His words on Sunday were even more emotive, and came with a ringing immediacy. His face as he stepped up to take the final penalty looked drained, but his nerve remained sure and he converted with a precise, low shot.

The tears then were from Aubameyang, distraught in the centre-circle. He has been one of the players of the tournament, a powerful and mobile forward who had come to embody his country's emergence as possible winners. Sylvia Bongo, the first lady, took to wearing an Aubameyang 9 shirt, as did a lot of the crowd. As he stepped up to take his penalty, his anxiety was obvious; it wasn't an awful shot, but neither was it particularly near the corner and Soumbeila Diakité saved relatively comfortably low to his left.

Aubameyang, eventually, was helped from the field by his father, himself a former Gabon international, and himself wearing a yellow T-shirt bearing his son's No9. Often tears on a football pitch feel self-indulgent, the spoiled multimillionaire brat bawling because he's missed out on yet another medal. Here, though, as the fans who remained gently applauded, it was easy to have sympathy for a man who clearly felt he had let his country down – and a country that will probably never have a better chance to win the Cup of Nations. Who can imagine the pressure when the president's wife wears your shirt?

Still, his pain was soon placed into context by Keita's words. "I'm appealing to the people to stop," Keita said. "It's not normal, we don't do that. We need peace, we are all Malians. The president of the republic needs to do the most he can to stop it. We are celebrating our win but at the same time we feel very sad. There is a sadness among the players."

The Tuareg have been fighting a separatist war in the north-east for years, with major outbreaks of fighting between 1990 and 1995 then from 2007 to 2009. They are a nomadic people, wandering across the desert regions of Algeria, Libya, Mali, Mauritania and Niger, largely ignoring national borders. Colonel Gadaffi sponsored that second uprising, intending to destabilise the government in Bamako.

After it was defeated, many of the rebels fled to Libya, where they helped shore up the Gadaffi regime. When Gadaffi fell, between 2,000 and 4,000 people – depending whose account you believe – fled across the border into the mountains of north-eastern Mali, laden with arms and cash. It's they who are behind the National Movement for the Liberation of Azawad (the north-eastern part of Mali comprising Timbuktu, Kidal and Gau). The Malian government accuses them of links with al-Qaida, although they deny it.

The NMLA has attacked towns in the region, and at least 20 people were killed in fighting around Timbuktu at the weekend. It's estimated 15,000 Malians have fled into neighbouring Niger and Mauritania, while rioting in Bamako – in protest at the army's inability to stop the NMLA – has led several Tuarag to flee the capital for fear of reprisals.

Among journalists there are two sorts of Cups of Nations veterans: those who say Burkina Faso 1998 was the best ever tournament and those who prefer Mali 2002. For those of us who remember what a happy, friendly place Mali was 10 years ago, the realisation of how bad the situation has become was particularly shocking. I remember Mopti – which proudly declared itself "the Venice of Africa" – as a sleepy town on the Niger, from where the ferry left for Timbuktu. George Weah played his final ever international there and, as the Liberia team bus drove across the causeway to the stadium, which stood in the middle of a marshy lagoon, he was welcomed by the local scout troop waving flags. Now the threat of kidnapping is so high that Mopti is a no-go area for foreigners. Half the country is effectively in a state of war.

Libya came to this tournament to play for unity, for their new government. Mali, too, are playing for their people. In pure footballing terms, they have been the least impressive of the four semi-finalists, and many neutrals probably felt a sense of disappointment at being denied a semi-final between Gabon and Ivory Coast. In front of a packed Stade de l'Amitié, that had the potential to be a classic; as it is, it's doubtful more than 3,000 to 4,000 will turn out for a game between François Zahoui's conservative Ivorians and Alain Giresse's dogged Mali. (Poor attendances are a perennial Cup of Nations issue: it's not just high ticket prices, although that clearly doesn't help, but also the fact that most of the population has no disposable income – and so any price would be too high – and, as Mark Gleeson, the doyen of African football journalists, pointed out, the absence of a football-going culture in most of Africa).

Mali, though, have shown great resolve in seeing off Guinea and holding off Gabon before finding a late equaliser – apparently drawing strength from the rumpled and phlegmatic figure of Giresse, who regards the pitch from the touchline with the weary resignation of a restaurateur surveying his last pair of customers after a long night. When they needed to, they found an extra gear to come from behind to beat Botswana. Ghana beat them comfortably enough, but Ivory Coast will have to do more than merely wait for mistakes, which is largely how they've played until now.